Harry Potter and the Shinobi World
by Woolleymammoth
Summary: A wish granted during a confluence of events, Harry Potter finds himself into a world that is far different then that which he had been born into. Found by the right person at the right time, will allow him to adapt and eventually change the world where destiny has no holds on him.


Standard Disclaimer of I dont own anything. All belongs to J.K and Kishimoto

This is the first a few new stories. I will be shooting to update them once a month. this has not been beta'd as i dont have an awesome person to do that for me. Constructive criticism is always welcomed. Flames are not. I will just end up pointing it out in the next chapter and internet shame that person. You dont like it, dont read it. that simple.

* * *

October 31, 1988

Little Whinging, Surrey, England

It was night and Halloween was a cursed day. That's all eight-year-old Harry Potter could really think of tonight. Every Halloween since he could remember has been cursed. Something would happen to either his Aunt Petunia or his Uncle Vernon that would set them off and he would end up with even less food and more of a beating. Last year some guy in a green robe bowed to him on the street, later that night he ended up getting hit with a frying pan. The year before that his teacher had yelled at him and he some how turned her hair blue.

This year his uncle had loss a major client at work. His uncle was a manager at Grunnings, the drill manufacture and sales company. His uncle couldn't understand that his client went somewhere else. Then again, the things Vernon Dursley couldn't comprehend would fill a list that could probably circle the globe…twice. It was this client loss that lead harry to his current situation, his hands tied to the banister right above his cupboard, shirtless and with gashes crisscrossing his back weeping fresh blood from his uncles belt, as tears streamed down his face, wishing with all his might that he could go anywhere but else.

"Please. Please someone, anyone. Help." The young boy whispered over and over as if it helped him focus on anything but the pain.

In the vast multiverse, where each choice of each person creates splinters, A universe where the choice was made one way and a choice where it was made the other way. In some universes you have a world where earth is technologically advanced, in other you have an earth where people have powers, some are mutants, some are aliens. Then you have worlds where there is a selection of the population which was born with an innate power called magic. And in those universes, you have Harry James Potter, Wizard. In many universes Harry Potter grows up wishing to be raised somewhere else by someone else. In some he is raised by his godfather, in some he is raised by a nice wizarding family of redheads, in others he is raised by a insane witch that escaped justice and in even more is raised by a group of evil magic users with blonde hair.

In many realities, Harry James Potters wish is never granted, however in one case a confluence of events happened. A meddling old man bound a powerful baby's magical core, cause it to strain and grow to heal its container. Seven years exactly since a deal was forged to care for a boy was broken. A shooting star passed over at the right moment. An accident many would have called it, but an accident is just the will of the universe expressing itself. And it was this universe's will that Harry James Potter be raised somewhere else.

Within Harrys body, the bindings that had been staining for years, finally burst and granted his wish and the shooting star provided direction. A rainbow of colored light surrounding the boy and with a bang that was multiplied by a hundred he was gone. The explosion that would destroy the entire house killing his last relatives would be put down as a gas leak that ignited.

xXx

October 31, 0281

The Village Hidden in the Leaves

Thirty-two-year-old Jiraiya was giggling as he leapt from tree to tree on his way back to Konoha, just thinking about finally being back in the village and get to do some more research at the hot springs. Many thinks of Jiraiya as a perverted ninja, who was decent in Fuinjutsu, was a spymaster and a sage. And they would be right, and when he started out, he decided to not hide his perverseness and would craft it into a mask. That mask lulled allies and enemies alike to drop their guard, allowing him to get information or strike easier.

As Jiraiya was contemplating whether to stop by the bathhouses for some research first or to stop and give the Hokage his report when the forest was disturbed by a flash of light and a wave of intense heat. Curious, since it was about a mile outside the village walls, Jiraiya head towards the disturbance. He searched until he heard whimpering and went towards the sound. He paused when he came upon a child that was covered in burns and blood in the middle of a perfect circle of scorched earth.

Jiraiya jumped down and came closer, as he did, he started taking note of the child. He immediately noted it was a boy, with black hair that seemed to have blood red towards the ends, with a pale skin tone that was littered with cuts and bruises. The back was torn and bleeding at what could only be whipping. Jiraiya could feel a weird energy around the circle that wasn't chakra or nature chakra. Jiraiya was many things and had done some horrible acts in the name of the greater good and others, but he still had a soft spot of children. He picked up the child and took to the trees going as fast as he could to the village so he could get to the hospital. As he was close to the child and holding him, he couldn't feel any chakra, however, he could feel some type of unknown energy.

After running for ten minutes and flaring his chakra in the correct code for priority emergency entry, he was through the gates heading to the hospital.

Jiraiya burst through the doors shouting. "Hime! Where are you Tsunade-hime?"

A very busty blonde with a purple diamond on her forehead came out of a room at hearing her former teammates cry. As she was about to tell him not to yell in a hospital and then punch him across the village, she saw a bloody lump in his arms, which after a few seconds realized it was a person and more specifically it was a child.

Tsunade turned to a nurse, "Get a gurney right away and prep a room"

The Nurse ran down the hall to get a gurney and came back when Jiraiya put the child on it and followed as it was rolled to a room that was full of medical equipment. He watched as Tsunade worked with her hands glowing green as she diagnosed and attempted to heal him.

"I am detecting, a broken arm, six broken ribs, a cracked jaw, several incorrectly healed fractures, and a high number of lacerations on his body, the ones on his back obviously the most recent. He is also malnourished. What the hell happened Jiraiya?" Tsunade asked as she moved his hands all over the boy trying to make sure she got all the injuries.

"I would like to know that as well Jiraiya. I was notified of your use of emergency code and when you didn't come to me, I figured I should come and see what the cause was." Said an aging man in white and red robes and hat with the kanji for Hokage on it, as he walked into the room. He was followed by a man with bright yellow hair inn a green vest and a woman with gorgeous red hair and wearing the same type of green vest.

"I found him on my way back to the Village from my latest mission. In the middle of a scorched circle about a mile form the village walls in the forest. I was in the trees when I saw a flash of light and felt a wave of intense heat. When I found he was still alive I picked him up and rushed here." Jiraiya explained as short and concisely as he could.

Tsunade's mind was going at the speed of light, cataloging injuries and prioritizing them so she can save the child. As she did that her mind came to a complete stop when it realized it wasn't finding a chakra network. Since the time of the Sage of Six paths all individuals produce chakra to some degree; those who run out of chakra completely will die. Produced within the "chakra coils" that mainly surround and connect to each chakra producing organ, the energy circulates throughout the body in a network called the "Chakra Pathway System", which is similar to the cardiovascular system. And yet she wasn't finding one in this child but could feel/sense something else. The more she focused on this second energy she could tell it was in his whole body but when she got to his forehead where there was a lightning bolt scar, she felt the same energy but incredibly malevolent.

Tsunade turned to one of the ANBU that came in with the Hokage. "Get me a Hyuuga here now and Get me a Yamanaka as well."

The ANBU hesitated for a moment and then left to do so, it was a common rule to listen to Tsunade as if you didn't you could end up through a wall from her punch. As the ANBU left, Tsunade had the nurse hook up an IV with fluids, antibiotics and TPN as well.

"Sensei, we still have the Head Monk from the Fire Temple here visiting correct?" Tsunade asked the old Hokage

"Yes, he isn't to leave for another two days, why?" responded Hiruzen Sarutobi

"There are some anomalies that I have found, and one of them has a very evil presence, can you please ask him to come here?" Tsunade asked her mentor and Hokage.

Hiruzen thought about it for a few moments and nodded, turned and left as the Head monk would require a personal visit to make the request.

xXx

From the moment that Harry came into this new world, his magic was Hypersensitive. IT was protective but also learning, after all magic is about emotions, will and instinct. As Harry was picked up his Magic didn't feel any ill intent coming form the man, it detected a large energy source, it felt of Fire, Earth, Transparency and Toads. It also felt nature coming from the man and all around them.

By the time Harrys magic was done cataloging this, it felt a woman this time and the green energy, which was analyzing and healing. Harrys magic felt the same large energy within the women, but felt healing, control, strength and slugs from her. Then more people came in. The old man that felt of earth, fire, water, wind and lighting. He also felt of monkeys. The younger man felt of wind, lighting, Toads and teleporting. The young woman was giving off so much that Harrys magic had to work in overdrive to catalog it, creation, pure energy, barriers, restraint, creation, destruction, inscriptions, a second energy source that was dwarfing all the other energies combined.

Harrys magic took all that information and went deeper and adding to its list of new things, it took over an hour to decipher that new information. Within that time, several more people had come and it learned even more. A woman with eyes that could see all and a man that came in that felt of mindwalking. It felt the man put its hand on its container and could tell it was reviewing its memories. Harrys magic scrutinized the mindwalker, reviewing how this worked and how to defend against it in the future if necessary.

While Harrys magic was analyzing the telepathy, the final Man came in that would finish Harrys transition to this world, changing fate and destinies of two worlds.

xXx

Hiruzen had just walked in with Head Monk Daisuke as Inoki Yamanaka finished his reviewing of the child's memories.

"What have you found Inoki?" The Hokage inquired

The Tall man shook his head like he was trying to shake unbelievable thought.

"What I saw in the child's mind angers me, astounds me, awes me and frightens me, Hokage-sama. I request that it waits until we are private. I believe you will be classifying it an S-Class secret." Inoki explained to the village leader in a somewhat dazed voice.

"Understood. Tsunade, Head monk Daisuke has graciously come to help in whatever you need." Hiruzen spoke to his student after thinking about Inoki's words.

"Daisuke-sama, please take a look at his forehead, while I was doing my diagnostic jutsu, when I came to it, I felt such malevolence, that I knew it could not be nature to the child." Tsunade explained to the elderly monk.

The Monk walked over, his curiosity piqued, and put his hand over the child's forehead. He immediately felt it, evil that had attached to the boy that should not be there. The Head monk also knew what it was, it was a soul or more specifically, it was a piece of a soul that had been complete and utterly corrupted. What he could not understand, was how it had happened. He did know that he had to detach it form the child.

"I will have to perform a spiritual cleansing immediately." Daisuke said after a few moments of contemplation.

"Impossible. We are still getting him stabilized. His body is broken, he is malnourished and would probably have died in hours if Jiraiya had not gotten him to us." Tsunade vehemently said.

"This is the best chance to do it now, and if we don't things could go very bad very fast once he is completely healed. I would not be surprised if that evilness is actually slowing or hindering the bodies natural healing and your efforts."

Tsunade and Daisuke stared at each other for nearly two minutes before Tsunade turned away and nodded.

"What do you need?"

"A free space for me and four of my fellow monks for us to work. This will take time and delicate." Said the old monk and after a moment of thought added "And please have a room with a bed for each of us, I have a feeling we will all be suffering from fatigue and chakra exhaustion afterwards."

"Understood. Give us an hour to set everything up." Tsunade hooked up a few more bags of fluids and TPN as it seemed the boys' body was seemingly pulling it in about nearly five times the rate it should and left the room.

Daisuke turned towards two others in the room "Minato-sama and Kushina-sama, would you please assist and set up seals that will contain all sounds and chakra from outside? Also block anyone from looking in with dojutsu or ninjutsu?"

"Of course, Daisuke-sama. We would be honored to help."

"Thank you. And Hokage-sama, I request to be apart of the meeting that the young Yamanaka said will be classified, I will explain what I found and what I will have done during it."

An hour later found Harry in the middle of an empty room surrounded by five monks. After the room was sealed off, daisuke begun instructing the monks on what they were going to do. It was a variation on the Destruction of Evil Seal Fuinjutsu, they were doing a Evil Cleansing. Going through three handseals and holding the Ram at the end, the ground lights up with green fuinjutsu surrounding Harry in a star pentagram with a circle of seals around it.

Within minutes of the jutsu being activated the boys body started toss and turn in contorting forms obviously form pain. The scar on the boys forehead started weeping blood and turned a vivid angry red as the boy's body was surrounded by an purple energy that started that the child's feet and slowing moving up the body sucking in the green chakra from the jutsu swirling and cleansing the boy. For over an hour the energy battled its way upwards destroying the entrenched soul, until finally it got to the forehead and then the real battle begun.

At the forehead was where the person known of Voldemort's unintended piece of his soul was entrenched since the night, he killed Harrys parents. It was the boys magic that kept the piece alive and on the mortal plane. It knew its destruction was imminent on an instinctual level and was fighting for every second. Finally Daisuke did something unexpected, he added the gift of the Hermit Group chakra to the jutsu, there was a lull in the jutsu the green fading and then it blazed with golden chakra that twisted and turned with Harrys purple magic and like a tsunami came down from all sides on the soul piece and destroyed it from existence. There wasn't a wail or a scream or even a Spector, it was just…gone.

xXx

In another universe a Beautiful blonde hair woman with shining silver eyes smiled as she felt the string that kept Voldemort alive snap. She felt the shade in Albania fade into the afterlife.

"Lily, your Son will now have a much better life, away from the plot of Albus too many made up names Bumblebore. It's a shame that my little moon won't be his wife this time, I guess that creature savant's grandson will have to do."

xXx

the moment that the soul piece was gone, Daisuke and his fellow monks stopped their jutsu and the other four collapsed immediately. Daisuke had enough energy to walk to the door and open it telling those waiting that it was done.

Tsunade and the nurses rushed in with gurneys so that they could all be moved. If she wasn't in Medic mode, her curiosity would have been through the roof on what happened.

xXx

Harry was unaware of the goings on around him, he was sitting in a white room. There were not even walls or a floor. He could not figure out what was going on. Many would have thought Harry Potter was a bit slow and uneducated based on his performance in school. They would be wrong. He wasn't a genius level IQ or have a photographic memory, but he was very smart and did have amazing recall speeds and while being scientific in his thinking, he thought outside the box. He hated boxes.

"Don't try to understand this place. It will give you a headache.' Spoke a feminine voice from behind him

Harry spun around and saw a beautiful woman with red hair and emerald eyes wearing a white robe. The same woman he had dreams of. His mother.

"I am sorry. I am so sorry, but I am not your mother. I am an echo of her, of her magic she used that night." Said the no identified Echo Lily

"What do you mean?" Harry asked while his thoughts had both stopped and raced ahead at the same time which should not have been possible.

"seven years ago, you were attacked. Your father was killed, I was killed, but not before I enacted a ritual of sacrifice to bind my magic to you, to protect you from the killing curse and the evil that was Voldemort."

"I am confused."

Echo Lily sighed and begun her tale. She told him about her life and the life of his father. She explained that they were users of magic and their time at Hogwarts. Of the war and the prophecy. How a friend came to her and warned her that a trusted wizard, the leader of the light Albus Dumbledore was meddling again. How Lily had to prepare for the worst. She delved into charms and rituals that were a millennium old. Until she found on that would allow her to protect him at the cost of her life.

"I am the remnant of that magic. I am the one that has been directing your magic to heal you as I strained against the bindings. Even now, I am directing your Magic to learn of this new world. And oh, what a different world it is."

Harry just stared at his not mother for what felt like a lifetime. "So, let me get this straight. I am a wizard. You were a witch. A probably fake prophecy said I was destined to defeat the Dark Lord. Somehow the said Dark Lord found out about the prophecy which caused you guys to go into hiding. Trusting the wrong friend and end up dying by the Dark Lord but not before you enacted a ritual that saved my life from an unblockable curse. And after living with your 'loving' sister for seven year by magic finally broke free and now I am in another dimension?"

'Yep. That's about it" chirped Echo Lily

"Great. I will probably breakdown over the next few days and have nightmares for months if not years. But I can't fix that now. Why are we meeting?" Harry asked.

"This should have and would never have happened but somehow a perfect storm of bad things happened and the incredibly luck of surviving everything allowed this to happen. You were on the very cusp of death. Between your weakened body, the beating last night, the dimensional travel and the spiritual cleansing of a piece of Voldemort soul, you nearly died. And because you didn't, it allowed your conscious and subconscious mind meld and allowed me to speak with you. We have to make the most of it because this won't happen again." Explained Echo Lily.

"Okay what do I need to know." Harry asked seriously, knowing that the next few moments were going to define his future.

"You are in another universe. And the humans here do not have magic. They have learned to harness and combine the spiritual and physical energy into what they call chakra. This allows them to do many things. The next thing you should know is that this world is a world of war. Each country has a civilian population and a warrior population. Here the warriors are ninja as in assassins and such." Echo Lily started to explain.

"While I could explain to you about the countries and such, that can be taught to you when you awake. We need to focus on the ninja arts. When chakra is used in the ninja arts it is called jutsu, which means skill/technique in their language. Jutsu is has many categories. However, the main three are Ninjutsu, Taijutsu and Genjutsu. Ninjutsu are basically the spells of the shinobi world. Taijutsu is the hand to hand combat and Genjutsu is there illusions."

"Wait. How do you know all of this?" Harry interrupted.

"The shinobi who scanned your memories. A door once open can be step through in either direction. As he watched your memories, I searched his. I didn't care for his secrets. I cared about knowledge and terms. To have references for everything your magic was sensing in its hypersensitive state." Echo Lily replied with a mischievous glint in her eyes

"Okay. Then let's go through it. What can we do with chakra?" Harry queried

"Absolutely nothing." Echo Lily responded back almost happily, causing harry to face palm.

"Then why are we having this conversation?"

"The Potters have been the vanguard against corruption, injustice and evil for over two thousand years. It's in your very blood. Whether you know it or not, you would eventually find yourself drifting towards being a warrior anywhere you went. You don't have chakra and I don't believe you can unlock it, but you have magic!" Echo Lily said quite seriously

"The way magicals of our world fought was quite different and frankly a shinobi would have slaughtered us because of it. But magic can adapt and so with this new world I can use the last remaining existence I have to have your magic grow and adapt. That is why we are discussing it."

"Make sense now. Please continue."

"first off your body, as long as the healer keeps providing nutrients your magic will be able to correct all the malnutrition and broken bones. While it is repairing that is will also allow for denser bones and muscles than what you were. We will also be able to fix your eyes now that the leach is gone. You won't be able to see through walls or copy people's movements with them, but you might be able to do a couple things. This will allow you to physically be able to keep up with the shinobi, and magic can boost it even more if you practice it. I have learned that there is a lot of elemental manipulation here, you will not have the same ability as them to. You will be able to wield the elements, but you have to be clever about it."

"You will be able to use their seals, as it is just another version of runes, but you will have to practice to tailor it to magic instead of chakra. Voldemort left a lot of knowledge when he was destroyed. Just like the knowledge from Inoki it won't be available to you like a book. It will come to you during sleep or an action triggers it or such. You will have to work hard, and you will have to endure. Also, some shinobi have the ability to take in chakra that is produced from nature, this is called nature chakra and allows for the use of Senjutsu. You will be able to take in magic from this world/dimension. We call that Sorcery. I would wait for a while before you do that."

"Some of the shinobi have contracts with what are called summoning animals. They are animals that have gained sentience because of chakra and formed clans based on species. Since you don't have chakra if you want something like this you will have to figure out an alternative. We are almost out of time harry. Know your mother and father loved you very much. Live in this world and find yourself a nice girl."

Echo Lily hugged harry even as the white world was getting brighter by the second, until he had to shut his eyes tightly as feeling and consciousness came back to him.

Harry opened his eyes to see this new world he found himself in.


End file.
